On 08/26/2011 10:18 AM, REX PALMER wrote:
Once waters have been located and refined is there a program that analyses
their positions
in terms of solvation shells?
Can the results be compared easily with those from related known
protein structures?
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
watertidy did this, albeit in a non-standard PDB nomenclature
It matches waters associated with chain A say into an associated CHAIN R
say with the matching residue number and a code to indicate whether it
is linked to N O OG ODi NDi ...
ie a water hydrogen bonded to N A 1 would be labelled OW0 R 1
a water hydrogen bonded to ND1 A 1 would be labelled OW4 R 1
etc.
Then you can link the atoms in CHAIN R to another set of labels in CHAIN S
However the PDB wont accept this!
